A Review

Ovarian cancer is the most common cause of death among gynecological malignancies. We discuss different types of clinical and nonclinical features that are used to study and analyze the differences between benign and malignant ovarian tumors. Computer-aided diagnostic (CAD) systems of high accuracy are being developed as an initial test for ovarian tumor classification instead of biopsy, which is the current gold standard diagnostic test. We also discuss different aspects of developing a reliable CAD system for the automated classification of ovarian cancer into benign and malignant types. A brief description of the commonly used classifiers in ultrasound-based CAD systems is also given

Evolutionary Computation and QSAR Research

[Abstract] The successful high throughput screening of molecule libraries for a specific biological property is one of the main improvements in drug discovery. The virtual molecular filtering and screening relies greatly on quantitative structure-activity relationship (QSAR) analysis, a mathematical model that correlates the activity of a molecule with molecular descriptors. QSAR models have the potential to reduce the costly failure of drug candidates in advanced (clinical) stages by filtering combinatorial libraries, eliminating candidates with a predicted toxic effect and poor pharmacokinetic profiles, and reducing the number of experiments. To obtain a predictive and reliable QSAR model, scientists use methods from various fields such as molecular modeling, pattern recognition, machine learning or artificial intelligence. QSAR modeling relies on three main steps: molecular structure codification into molecular descriptors, selection of relevant variables in the context of the analyzed activity, and search of the optimal mathematical model that correlates the molecular descriptors with a specific activity. Since a variety of techniques from statistics and artificial intelligence can aid variable selection and model building steps, this review focuses on the evolutionary computation methods supporting these tasks. Thus, this review explains the basic of the genetic algorithms and genetic programming as evolutionary computation approaches, the selection methods for high-dimensional data in QSAR, the methods to build QSAR models, the current evolutionary feature selection methods and applications in QSAR and the future trend on the joint or multi-task feature selection methods.Instituto de Salud Carlos III, PIO52048Instituto de Salud Carlos III, RD07/0067/0005Ministerio de Industria, Comercio y Turismo; TSI-020110-2009-53)Galicia. Consellería de Economía e Industria; 10SIN105004P

Feature Space Augmentation: Improving Prediction Accuracy of Classical Problems in Cognitive Science and Computer Vison

The prediction accuracy in many classical problems across multiple domains has seen a rise since computational tools such as multi-layer neural nets and complex machine learning algorithms have become widely accessible to the research community. In this research, we take a step back and examine the feature space in two problems from very different domains. We show that novel augmentation to the feature space yields higher performance. Emotion Recognition in Adults from a Control Group: The objective is to quantify the emotional state of an individual at any time using data collected by wearable sensors. We define emotional state as a mixture of amusement, anger, disgust, fear, sadness, anxiety and neutral and their respective levels at any time. The generated model predicts an individual’s dominant state and generates an emotional spectrum, 1x7 vector indicating levels of each emotional state and anxiety. We present an iterative learning framework that alters the feature space uniquely to an individual’s emotion perception, and predicts the emotional state using the individual specific feature space. Hybrid Feature Space for Image Classification: The objective is to improve the accuracy of existing image recognition by leveraging text features from the images. As humans, we perceive objects using colors, dimensions, geometry and any textual information we can gather. Current image recognition algorithms rely exclusively on the first 3 and do not use the textual information. This study develops and tests an approach that trains a classifier on a hybrid text based feature space that has comparable accuracy to the state of the art CNN’s while being significantly inexpensive computationally. Moreover, when combined with CNN’S the approach yields a statistically significant boost in accuracy. Both models are validated using cross validation and holdout validation, and are evaluated against the state of the art

Selected Works in Bioinformatics

This book consists of nine chapters covering a variety of bioinformatics subjects, ranging from database resources for protein allergens, unravelling genetic determinants of complex disorders, characterization and prediction of regulatory motifs, computational methods for identifying the best classifiers and key disease genes in large-scale transcriptomic and proteomic experiments, functional characterization of inherently unfolded proteins/regions, protein interaction networks and flexible protein-protein docking. The computational algorithms are in general presented in a way that is accessible to advanced undergraduate students, graduate students and researchers in molecular biology and genetics. The book should also serve as stepping stones for mathematicians, biostatisticians, and computational scientists to cross their academic boundaries into the dynamic and ever-expanding field of bioinformatics

Ny forståelse av gasshydratfenomener og naturlige inhibitorer i råoljesystemer gjennom massespektrometri og maskinlæring

Gas hydrates represent one of the main flow assurance issues in the oil and gas industry as they can cause complete blockage of pipelines and process equipment, forcing shut downs. Previous studies have shown that some crude oils form hydrates that do not agglomerate or deposit, but remain as transportable dispersions. This is commonly believed to be due to naturally occurring components present in the crude oil, however, despite decades of research, their exact structures have not yet been determined. Some studies have suggested that these components are present in the acid fractions of the oils or are related to the asphaltene content of the oils. Crude oils are among the worlds most complex organic mixtures and can contain up to 100 000 different constituents, making them difficult to characterise using traditional mass spectrometers. The high mass accuracy of Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) yields a resolution greater than traditional techniques, making FT-ICR MS able to characterise crude oils to a greater extent, and possibly identify hydrate active components. FT-ICR MS spectra usually contain tens of thousands of peaks, and data treatment methods able to find underlying relationships in big data sets are required. Machine learning and multivariate statistics include many methods suitable for big data. A literature review identified a number of promising methods, and the current status for the use of machine learning for analysis of gas hydrates and FT-ICR MS data was analysed. The literature study revealed that although many studies have used machine learning to predict thermodynamic properties of gas hydrates, very little work have been done in analysing gas hydrate related samples measured by FT-ICR MS. In order to aid their identification, a successive accumulation procedure for increasing the concentrations of hydrate active components was developed by SINTEF. Comparison of the mass spectra from spiked and unspiked samples revealed some peaks that increased in intensity over the spiking levels. Several classification methods were used in combination with variable selection, and peaks related to hydrate formation were identified. The corresponding molecular formulas were determined, and the peaks were assumed to be related to asphaltenes, naphthenes and polyethylene glycol. To aid the characterisation of the oils, infrared spectroscopy (both Fourier Transform infrared and near infrared) was combined with FT-ICR MS in a multiblock analysis to predict the density of crude oils. Two different strategies for data fusion were attempted, and sequential fusion of the blocks achieved the highest prediction accuracy both before and after reducing the dimensions of the data sets by variable selection. As crude oils have such complex matrixes, samples are often very different, and many methods are not able to handle high degrees of variations or non-linearities between the samples. Hierarchical cluster-based partial least squares regression (HC-PLSR) clusters the data and builds local models within each cluster. HC-PLSR can thus handle non-linearities between clusters, but as PLSR is a linear model the data is still required to be locally linear. HC-PLSR was therefore expanded into deep learning (HC-CNN and HC-RNN) and SVR (HC-SVR). The deep learning-based models outperformed HC-PLSR for a data set predicting average molecular weights from hydrolysed raw materials. The analysis of the FT-ICR MS spectra revealed that the large amounts of information contained in the data (due to the high resolution) can disturb the predictive models, but the use of variable selection counteracts this effect. Several methods from machine learning and multivariate statistics were proven valuable for prediction of various parameters from FT-ICR MS using both classification and regression methods.Gasshydrater er et av hovedproblemene for Flow assurance i olje- og gassnæringen ettersom at de kan forårsake blokkeringer i oljerørledninger og prosessutstyr som krever at systemet må stenges ned. Tidligere studier har vist at noen råoljer danner hydrater som ikke agglomererer eller avsetter, men som forblir som transporterbare dispersjoner. Dette antas å være på grunn av naturlig forekommende komponenter til stede i råoljen, men til tross for årevis med forskning er deres nøyaktige strukturer enda ikke bestemt i detalj. Noen studier har indikert at disse komponentene kan stamme fra syrefraksjonene i oljen eller være relatert til asfalteninnholdet i oljene. Råoljer er blant verdens mest komplekse organiske blandinger og kan inneholde opptil 100 000 forskjellige bestanddeler, som gjør dem vanskelig å karakterisere ved bruk av tradisjonelle massespektrometre. Den høye masseoppløsningen Fourier-transform ion syklotron resonans massespektrometri (FT-ICR MS) gir en høyere oppløsning enn tradisjonelle teknikker, som gjør FT-ICR MS i stand til å karakterisere råoljer i større grad og muligens identifisere hydrataktive komponenter. FT-ICR MS spektre inneholder vanligvis titusenvis av topper, og det er nødvendig å bruke databehandlingsmetoder i stand til å håndtere store datasett, med muligheter til å finne underliggende forhold for å analysere spektrene. Maskinlæring og multivariat statistikk har mange metoder som er passende for store datasett. En litteratur studie identifiserte flere metoder og den nåværende statusen for bruken av maskinlæring for analyse av gasshydrater og FT-ICR MS data. Litteraturstudien viste at selv om mange studier har brukt maskinlæring til å predikere termodynamiske egenskaper for gasshydrater, har lite arbeid blitt gjort med å analysere gasshydrat relaterte prøver målt med FT-ICR MS. For å bistå identifikasjonen ble en suksessiv akkumuleringsprosedyre for å øke konsentrasjonene av hydrataktive komponenter utviklet av SINTEF. Sammenligninger av massespektrene fra spikede og uspikede prøver viste at noen topper økte sammen med spikingnivåene. Flere klassifikasjonsmetoder ble brukt i kombinasjon med ariabelseleksjon for å identifisere topper relatert til hydratformasjon. Molekylformler ble bestemt og toppene ble antatt å være relatert til asfaltener, naftener og polyetylenglykol. For å bistå karakteriseringen av oljene ble infrarød spektroskopi inkludert med FT-ICR MS i en multiblokk analyse for å predikere tettheten til råoljene. To forskjellige strategier for datafusjonering ble testet og sekvensiell fusjonering av blokkene oppnådde den høyeste prediksjonsnøyaktigheten både før og etter reduksjon av datasettene med bruk av variabelseleksjon. Ettersom råoljer har så kompleks sammensetning, er prøvene ofte veldig forskjellige og mange metoder er ikke egnet for å håndtere store variasjoner eller ikke-lineariteter mellom prøvene. Hierarchical cluster-based partial least squares regression (HCPLSR) grupperer dataene og lager lokale modeller for hver gruppe. HC-PLSR kan dermed håndtere ikke-lineariteter mellom gruppene, men siden PLSR er en lokal modell må dataene fortsatt være lokalt lineære. HC-PLSR ble derfor utvidet til convolutional neural networks (HC-CNN) og recurrent neural networks (HC-RNN) og support vector regression (HC-SVR). Disse dyp læring metodene utkonkurrerte HC-PLSR for et datasett som predikerte gjennomsnittlig molekylvekt fra hydrolyserte råmaterialer. Analysen av FT-ICR MS spektre viste at spektrene inneholder veldig mye informasjon. Disse store mengdene med data kan forstyrre prediksjonsmodeller, men bruken av variabelseleksjon motvirket denne effekten. Flere metoder fra maskinlæring og multivariat statistikk har blitt vist å være nyttige for prediksjon av flere parametere from FT-ICR MS data ved bruk av både klassifisering og regresjon